Index: src/hg/lib/genomicSuperDups.as
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/genomicSuperDups.as,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/lib/genomicSuperDups.as	3 Feb 2006 19:08:42 -0000	1.2
+++ src/hg/lib/genomicSuperDups.as	8 Feb 2010 19:43:43 -0000	1.3
@@ -1,31 +1,33 @@
 table genomicSuperDups
 "Summary of large genomic Duplications (>1KB >90% similar)"
   (
   string chrom;       "Reference sequence chromosome or scaffold"
   uint chromStart;   "Start position in chromosome"
   uint chromEnd;     "End position in chromosome"
   string name;         "Other chromosome involved"
   uint score;        "Score from 900-1000.  1000 is best"
   char[1] strand;       "Value should be + or -"
   string otherChrom;   "Other chromosome or scaffold"
   uint otherStart;   "Start in other  sequence"
   uint otherEnd;     "End in other  sequence"
-  uint otherSize;    "Total size of other sequence"
-  uint uid;       "unique id"
-  uint posBasesHit;       "HitPositive UnCovered"
-  string testResult;       "HitPositive (yes or no) UnCovered (covered=0)"
-  string verdict;       "Real or Allele"
+  uint otherSize;    "Total size of other sequence (otherEnd - otherStart)"
+  uint uid;       "Unique id shared by the query and subject"
+  uint posBasesHit;       "For future use"
+  string testResult;       "For future use"
+  string verdict;       "For future use"
+  string chits;       "For future use"
+  string ccov;       "For future use"
   string alignfile;       "alignment file path"
   uint alignL;       "spaces/positions in alignment"
   uint indelN;       "number of indels"
   uint indelS;       "indel spaces"
   uint alignB;       "bases Aligned"
   uint matchB;       "aligned bases that match"
   uint mismatchB;    "aligned bases that do not match"
   uint transitionsB;    "number of transitions"
   uint transversionsB;    "number of transversions"
   float fracMatch;    "fraction of matching bases"
   float fracMatchIndel;    "fraction of matching bases with indels"
   float jcK;          "K-value calculated with Jukes-Cantor"
   float k2K;          "Kimura K"
   )

